Contacts of the helix formed by residues 509 - 531 (chain A) in PDB entry 4BSN
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 509 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A SER* 5.7 3.6 - - - -
469A TYR* 4.2 26.5 + + - -
507A ALA 5.4 3.1 - - - -
508A MET* 1.3 76.6 - - - +
510A GLU* 1.3 55.5 + - - +
511A GLU* 3.4 11.2 - - + +
512A ASP* 3.2 21.3 + - - +
513A GLU* 2.7 35.9 + - - +
553A ARG* 4.0 1.1 - - - +
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Residues in contact with GLU 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509A HIS* 1.3 72.7 - - - +
511A GLU* 1.3 59.0 + - - +
513A GLU* 3.8 1.2 - - - +
514A LYS* 3.0 31.9 + - - +
553A ARG* 3.3 21.5 - - - +
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Residues in contact with GLU 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509A HIS* 4.8 9.1 - - + +
510A GLU* 1.3 79.3 - - - +
512A ASP* 1.3 73.1 + - - +
514A LYS* 4.3 12.6 + - - +
515A ARG* 3.8 19.2 + - - +
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Residues in contact with ASP 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A TYR* 3.5 31.9 + - + -
508A MET* 4.2 18.7 - - + +
509A HIS* 3.2 21.2 + - - +
511A GLU* 1.3 89.2 - - - +
513A GLU* 1.3 65.7 - - - +
514A LYS 3.3 0.7 - - - -
515A ARG* 3.6 23.0 + - - +
516A PHE* 3.1 24.9 + - - +
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Residues in contact with GLU 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504A ILE 5.2 0.3 - - - +
506A GLY 3.8 10.5 + - - -
508A MET* 3.3 27.8 + - + +
509A HIS 2.7 20.7 + - - +
510A GLU* 3.3 4.2 + - - +
512A ASP* 1.3 71.4 - - - +
514A LYS* 1.3 59.2 + - - +
516A PHE* 3.9 5.4 - - + +
517A LEU* 2.9 39.8 + - + +
551A TYR* 3.3 40.8 + - + -
553A ARG* 2.6 43.3 + - - +
554A PHE* 4.8 6.0 - - + +
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Residues in contact with LYS 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510A GLU 3.0 15.9 + - - +
511A GLU* 4.3 12.5 + - - +
513A GLU* 1.3 77.1 - - - +
515A ARG* 1.3 82.2 + - - +
518A VAL* 3.1 32.1 + - + +
554A PHE* 3.6 18.8 - - + -
558A HIS* 3.3 37.5 - - + +
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Residues in contact with ARG 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A TYR* 5.9 1.8 - - - -
473A GLU* 2.8 41.9 + - - -
511A GLU 3.8 13.7 + - - +
512A ASP* 3.6 29.3 + - - +
514A LYS* 1.3 92.6 - - - +
516A PHE* 1.3 59.8 + - - +
518A VAL* 3.3 17.9 - - - +
519A THR* 3.5 10.7 + - - -
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Residues in contact with PHE 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A GLU* 3.5 52.9 - - + +
476A MET* 4.1 30.3 - - + -
477A THR* 3.8 10.1 - - - -
501A ILE* 4.6 17.0 - - + -
504A ILE* 6.0 2.9 - - + -
508A MET* 4.3 24.9 - - + -
512A ASP 3.1 18.5 + - - +
513A GLU* 3.9 5.6 - - + +
515A ARG* 1.3 78.7 - - - +
517A LEU* 1.3 69.3 + - + +
519A THR* 3.5 8.4 + - - -
520A VAL* 3.3 40.0 + - + +
551A TYR* 5.6 4.5 - + - -
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Residues in contact with LEU 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A ILE* 4.7 8.7 - - + -
513A GLU* 2.9 21.3 + - + +
514A LYS 4.2 1.1 - - - +
516A PHE* 1.3 80.9 - - + +
518A VAL* 1.3 60.1 + - - +
520A VAL* 3.1 19.4 + - + +
521A ILE* 2.9 44.7 + - + +
547A ILE* 5.1 5.2 - - + +
551A TYR* 3.6 52.7 - - + -
554A PHE* 3.7 31.6 - - + -
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Residues in contact with VAL 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A LYS* 3.1 23.6 + - + +
515A ARG* 3.3 15.7 - - - +
517A LEU* 1.3 77.2 - - - +
519A THR* 1.3 67.5 + - - +
521A ILE* 3.9 1.2 - - - +
522A LYS* 3.1 26.2 + - + +
554A PHE* 4.3 10.5 - - + -
561A PHE* 3.7 32.4 - - + -
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Residues in contact with THR 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477A THR* 5.7 8.3 - - + -
480A LEU* 6.5 0.4 - - + -
481A HIS* 5.6 6.1 - - - +
515A ARG 3.5 12.3 + - - -
516A PHE* 3.5 9.4 + - - -
517A LEU 3.2 0.2 - - - -
518A VAL* 1.3 79.4 - - - +
520A VAL* 1.3 67.1 + - + +
522A LYS* 3.5 3.9 + - - +
523A ASP* 3.0 46.0 + - - +
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Residues in contact with VAL 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A LEU* 3.8 34.6 - - + +
497A LEU* 5.8 0.7 - - + -
501A ILE* 4.7 6.5 - - + -
516A PHE* 3.3 43.1 - - + +
517A LEU* 3.1 15.4 + - + +
519A THR* 1.3 77.6 - - + +
521A ILE* 1.3 58.6 + - + +
523A ASP* 3.9 2.2 - - - +
524A LEU* 3.0 34.9 + - + +
547A ILE* 3.8 28.7 - - + -
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Residues in contact with ILE 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A LEU* 2.9 38.9 + - + +
518A VAL 3.9 0.7 - - - +
520A VAL* 1.3 76.6 - - + +
522A LYS* 1.3 58.5 - - - +
524A LEU* 3.1 6.5 + - + +
525A LEU* 2.9 48.8 + - + +
544A ILE* 4.4 11.2 - - + -
547A ILE* 4.7 11.2 - - + +
548A VAL* 4.2 24.7 - - + -
554A PHE* 5.1 0.9 - - + -
555A LEU* 6.5 0.7 - - + -
561A PHE* 3.5 39.3 - - + -
565A VAL* 5.5 6.7 - - + -
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Residues in contact with LYS 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A VAL* 3.1 18.3 + - + +
519A THR* 3.9 5.2 - - - +
521A ILE* 1.3 80.7 - - - +
523A ASP* 1.3 63.1 + - - +
525A LEU* 3.3 10.2 + - - +
526A GLY* 3.1 23.9 + - - -
561A PHE* 5.3 1.1 - - + -
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Residues in contact with ASP 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A LEU* 5.3 12.5 - - + +
481A HIS* 4.1 18.2 + - - -
484A VAL* 3.7 34.1 - - + +
519A THR* 3.0 32.6 + - - +
520A VAL* 4.1 3.8 - - - +
522A LYS* 1.3 80.6 - - - +
524A LEU* 1.3 57.6 + - - +
526A GLY* 3.9 2.3 - - - +
527A LEU* 3.0 26.9 + - - +
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Residues in contact with LEU 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A LEU* 5.8 7.8 - - + +
494A LEU* 5.1 9.2 - - + -
498A CYS* 4.3 18.2 - - - -
520A VAL* 3.0 23.2 + - + +
521A ILE* 3.1 8.2 + - - +
523A ASP* 1.3 76.5 - - - +
525A LEU* 1.3 59.7 + - - +
527A LEU* 3.4 7.1 + - + +
528A CYS* 3.0 25.1 + - - +
540A ILE* 4.0 20.0 - - + +
543A ASN* 5.2 0.9 - - + -
544A ILE* 3.7 34.7 - - + +
547A ILE* 3.8 33.4 - - + -
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Residues in contact with LEU 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A ILE* 2.9 33.6 + - + +
522A LYS* 3.3 10.3 + - - +
524A LEU* 1.3 76.5 - - - +
526A GLY* 1.3 60.6 + - - +
528A CYS* 3.2 11.1 + - + +
529A GLU* 3.1 24.9 + - - +
544A ILE* 4.6 20.0 - - + -
561A PHE* 6.2 0.2 - - + -
564A THR* 5.0 17.0 - - + -
568A LYS* 4.7 24.5 - - + +
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Residues in contact with GLY 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A VAL* 6.5 0.9 - - - -
522A LYS 3.1 14.6 + - - -
523A ASP* 3.9 2.7 - - - -
524A LEU 3.3 0.2 - - - -
525A LEU* 1.3 74.6 - - - +
527A LEU* 1.3 58.1 + - - +
529A GLU* 3.2 9.2 + - - +
530A GLN* 3.0 28.1 + - - +
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Residues in contact with LEU 527 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483A GLN* 3.3 31.4 - - + +
484A VAL* 3.7 22.4 - - + +
489A TRP* 3.8 24.5 - - + +
494A LEU* 4.2 12.3 - - + -
523A ASP 3.0 16.6 + - - +
524A LEU* 3.5 13.2 - - + +
525A LEU 3.2 0.2 - - - -
526A GLY* 1.3 76.5 - - - +
528A CYS* 1.3 63.5 + - - +
530A GLN* 3.5 14.4 + - - +
531A LYS* 3.1 21.7 + - - +
540A ILE* 3.7 25.4 - - + -
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Residues in contact with CYS 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A LEU 3.0 13.5 + - - +
525A LEU* 3.2 16.4 + - + +
527A LEU* 1.3 78.3 - - - +
529A GLU* 1.3 60.4 + - - +
531A LYS* 3.5 14.6 - - - +
537A LYS* 5.6 8.2 - - - +
540A ILE* 3.6 28.0 - - + +
541A ALA 5.5 0.4 - - - -
544A ILE* 6.3 1.8 - - + -
568A LYS* 5.7 5.6 - - - -
572A PHE* 3.9 29.6 - - - -
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Residues in contact with GLU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A LEU 3.1 12.4 + - - +
526A GLY* 3.5 12.6 - - - +
527A LEU 3.2 0.2 - - - -
528A CYS* 1.3 78.2 - - - +
530A GLN* 1.3 64.4 + - - +
531A LYS 3.9 4.0 - - - +
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Residues in contact with GLN 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A VAL* 3.6 21.6 + - - +
485A ASN 5.0 3.0 + - - -
486A GLY* 4.9 7.7 - - - -
489A TRP* 4.0 25.9 - - + -
526A GLY 3.0 15.8 + - - +
527A LEU* 4.0 12.6 - - - +
529A GLU* 1.3 78.0 - - - +
531A LYS* 1.3 65.3 + - - +
532A ARG* 3.4 6.4 + - - +
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Residues in contact with LYS 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A TRP* 3.5 30.7 - - + -
527A LEU 3.1 15.8 + - - +
528A CYS 3.5 14.8 - - - +
529A GLU 3.4 3.8 - - - +
530A GLN* 1.3 80.4 - - - +
532A ARG* 1.3 59.1 + - - +
533A GLY 5.2 0.7 - - - +
536A ASN* 3.7 20.0 - - + +
537A LYS* 5.1 4.7 + - - +
540A ILE* 4.3 10.5 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il